
# Create a temporary directory to hold notebook output, and change the working directory to that directory.
from tempfile import TemporaryDirectory
import os
import shutil
data_dir = TemporaryDirectory()

os.chdir(data_dir.name)


import os
if 'CRDS_CACHE_TYPE' in os.environ:
    if os.environ['CRDS_CACHE_TYPE'] == 'local':
        os.environ['CRDS_PATH'] = os.path.join(os.environ['HOME'], 'crds', 'cache')
    elif os.path.isdir(os.environ['CRDS_CACHE_TYPE']):
        os.environ['CRDS_PATH'] = os.environ['CRDS_CACHE_TYPE']
print('CRDS cache location: {}'.format(os.environ['CRDS_PATH']))

CRDS cache location: /grp/crds/cache


import warnings
import psutil
from astropy.io import fits

# Only print a DeprecationWarning the first time it shows up, not every time.
with warnings.catch_warnings():
    warnings.simplefilter("once", category=DeprecationWarning)
    import jwst
    from jwst.pipeline.calwebb_detector1 import Detector1Pipeline
    from jwst.assign_wcs.assign_wcs_step import AssignWcsStep
    from jwst.msaflagopen.msaflagopen_step import MSAFlagOpenStep
    from jwst.extract_2d.extract_2d_step import Extract2dStep
    from jwst.srctype.srctype_step import SourceTypeStep
    from jwst.wavecorr.wavecorr_step import WavecorrStep
    from jwst.flatfield.flat_field_step import FlatFieldStep
    from jwst.pathloss.pathloss_step import PathLossStep
    from jwst import datamodels

# The latest version of NPTT is installed in the requirements text file at:
# /jwst_validation_notebooks/environment.yml

# import NPTT
import nirspec_pipe_testing_tool as nptt

# To get data from Artifactory
from ci_watson.artifactory_helpers import get_bigdata


# Make sure that the version used is the right one

pipeline_version = jwst.__version__
nptt_version = nptt.__version__

print("Using jwst pipeline version: ", pipeline_version)
print("Using NPTT version: ", nptt_version)

Using jwst pipeline version:  1.8.2
Using NPTT version:  2.0.1


testing_data = {
                
                'ifu_prism_clear':{
                                  'uncal_file_nrs1': 'ifu_prism_nrs1_uncal.fits',
                                  'uncal_file_nrs2': 'ifu_prism_nrs2_uncal.fits',
                                  'msa_shutter_config': None }
                                
               }


# define function to pull data from Artifactory
def get_artifactory_file(data_set_dict, detector):
    """This function creates a list with all the files needed per detector to run the test.
    Args:
        data_set_dict: dictionary, contains inputs for a specific mode and configuration
        detector: string, either nrs1 or nrs2
    Returns:
        data: list, contains all files needed to run test
    """
    files2obtain = ['uncal_file_nrs1', 'msa_shutter_config']
    data = []
    for file in files2obtain:
        data_file = None
        try: 
            if '_nrs' in file and '2' in detector:
                file = file.replace('_nrs1', '_nrs2')

            data_file = get_bigdata('jwst_validation_notebooks',
                                         'validation_data',
                                         'nirspec_data', 
                                         data_set_dict[file])
        except TypeError:
            data.append(None)
            continue

        data.append(data_file)

    return data


# Set common NPTT switches for this test

# accepted threshold difference with respect to benchmark files
threshold_diff = 9.999e-05

# other NPTT variables
writefile = False
show_figs = True
save_figs = False

# Get the data
detectors = ['nrs1', 'nrs2']
results_dict = {}
for mode_config, data_set_dict in testing_data.items():
    for det in detectors:
        print('Testing files for detector: ', det)
        data = get_artifactory_file(data_set_dict, det)
        uncal_file, msa_shutter_config = data
        print('Working with uncal_file: ', uncal_file)
        uncal_basename = os.path.basename(uncal_file)
        
        # Run the stage 1 pipeline 
        rate_object = Detector1Pipeline.call(uncal_file)
        # Make sure the MSA shutter configuration file is set up correctly
        rate_object.meta.instrument.msa_metadata_file = msa_shutter_config
        if msa_shutter_config is not None:
            rate_object.meta.instrument.msa_metadata_file = msa_shutter_config
            print('MSA shutter configuration file: ', rate_object.meta.instrument.msa_metadata_file)

        # Run the stage 2 pipeline steps
        try:
            pipe_object = AssignWcsStep.call(rate_object)
            skip_file = False
        except:
            print('An error occurred that made the pipeline crash, probably: No open slits fall on detector ', det)
            print("Skipping test for this file. \n")
            skip_file = True
            
        result_msg = 'skipped'
        if not skip_file:                        
            if 'ifu' in uncal_basename.lower() or 'mos' in uncal_basename.lower():
                pipe_object = MSAFlagOpenStep.call(pipe_object)
            if 'ifu' not in uncal_basename.lower():
                pipe_object = Extract2dStep.call(pipe_object)
            pipe_object = SourceTypeStep.call(pipe_object)
            pipe_object = WavecorrStep.call(pipe_object)
            flat_field_object = FlatFieldStep.call(pipe_object)
            pathloss_object = PathLossStep.call(flat_field_object)

            # get the corresponding reference file from the pathloss datamodel
            reffile_path = pathloss_object.meta.ref_file.pathloss.name.replace("crds://", 
                                                    "https://jwst-crds.stsci.edu/unchecked_get/references/jwst/")

            # Run the validation test
            %matplotlib inline

            if 'fs' in uncal_file.lower():
                print('Running test for FS...')
                
                source_type = pathloss_object.meta.target.source_type
                
                if source_type == 'POINT' or source_type is None:
                    median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_ps.pathtest(
                                                                                         flat_field_object, 
                                                                                         reffile_path,
                                                                                         pathloss_object,
                                                                                         writefile=writefile,
                                                                                         show_figs=show_figs,
                                                                                         save_figs=save_figs,
                                                                                         threshold_diff=threshold_diff)
                else:
                    median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_fs_uni.pathtest(
                                                                                         flat_field_object, 
                                                                                         reffile_path,
                                                                                         pathloss_object,
                                                                                         writefile=writefile, 
                                                                                         show_figs=show_figs,
                                                                                         save_figs=save_figs,
                                                                                         threshold_diff=threshold_diff)

            if 'mos' in uncal_file.lower():
                print('Running test for MOS...')
                median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_mos.pathtest(
                                                                                     flat_field_object, 
                                                                                     reffile_path,
                                                                                     pathloss_object,
                                                                                     writefile=writefile,
                                                                                     show_figs=show_figs,
                                                                                     save_figs=save_figs,
                                                                                     threshold_diff=threshold_diff)

            if 'ifu' in uncal_file.lower():
                print('Running test for IFU...')

                if pathloss_object.meta.target.source_type == 'POINT':
                    median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_ifu_ps.pathtest(
                                                                                         flat_field_object, 
                                                                                         reffile_path,
                                                                                         pathloss_object,
                                                                                         writefile=writefile,
                                                                                         show_figs=show_figs,
                                                                                         save_figs=save_figs,
                                                                                         threshold_diff=threshold_diff)
                else:
                    median_diff, result_msg, log_msgs = nptt.calwebb_spec2_pytests.auxiliary_code.pathloss_ifu_uni.pathtest(
                                                                                         flat_field_object, 
                                                                                         reffile_path,
                                                                                         pathloss_object,
                                                                                         writefile=writefile, 
                                                                                         show_figs=show_figs,
                                                                                         save_figs=save_figs,
                                                                                         threshold_diff=threshold_diff)

        # Did the test passed 
        print("Did pathloss validation test passed? ", result_msg, "\n\n")
        rd = {uncal_basename: result_msg}
        results_dict.update(rd)
        
        # close all open files
        psutil.Process().open_files()
        closing_files = []
        for fd in psutil.Process().open_files():
            if data_dir.name in fd.path:
                closing_files.append(fd)
        for fd in closing_files:
            try:
                print('Closing file: ', fd)
                open(fd.fd).close()
            except:
                print('File already closed: ', fd)

Testing files for detector:  nrs1
Working with uncal_file:  /internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx/ifu_prism_nrs1_uncal.fits

2022-12-04 01:51:01,274 - stpipe - INFO - PARS-DETECTOR1PIPELINE parameters found: /grp/crds/cache/references/jwst/jwst_nirspec_pars-detector1pipeline_0004.asdf
2022-12-04 01:51:01,300 - stpipe.Detector1Pipeline - INFO - Detector1Pipeline instance created.
2022-12-04 01:51:01,302 - stpipe.Detector1Pipeline.group_scale - INFO - GroupScaleStep instance created.
2022-12-04 01:51:01,303 - stpipe.Detector1Pipeline.dq_init - INFO - DQInitStep instance created.
2022-12-04 01:51:01,304 - stpipe.Detector1Pipeline.saturation - INFO - SaturationStep instance created.
2022-12-04 01:51:01,305 - stpipe.Detector1Pipeline.ipc - INFO - IPCStep instance created.
2022-12-04 01:51:01,306 - stpipe.Detector1Pipeline.superbias - INFO - SuperBiasStep instance created.
2022-12-04 01:51:01,308 - stpipe.Detector1Pipeline.refpix - INFO - RefPixStep instance created.
2022-12-04 01:51:01,309 - stpipe.Detector1Pipeline.rscd - INFO - RscdStep instance created.
2022-12-04 01:51:01,310 - stpipe.Detector1Pipeline.firstframe - INFO - FirstFrameStep instance created.
2022-12-04 01:51:01,311 - stpipe.Detector1Pipeline.lastframe - INFO - LastFrameStep instance created.
2022-12-04 01:51:01,312 - stpipe.Detector1Pipeline.linearity - INFO - LinearityStep instance created.
2022-12-04 01:51:01,313 - stpipe.Detector1Pipeline.dark_current - INFO - DarkCurrentStep instance created.
2022-12-04 01:51:01,314 - stpipe.Detector1Pipeline.reset - INFO - ResetStep instance created.
2022-12-04 01:51:01,315 - stpipe.Detector1Pipeline.persistence - INFO - PersistenceStep instance created.
2022-12-04 01:51:01,317 - stpipe.Detector1Pipeline.jump - INFO - JumpStep instance created.
2022-12-04 01:51:01,318 - stpipe.Detector1Pipeline.ramp_fit - INFO - RampFitStep instance created.
2022-12-04 01:51:01,319 - stpipe.Detector1Pipeline.gain_scale - INFO - GainScaleStep instance created.
2022-12-04 01:51:01,491 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline running with args ('/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx/ifu_prism_nrs1_uncal.fits',).
2022-12-04 01:51:01,501 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_calibrated_ramp': False, 'steps': {'group_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dq_init': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'saturation': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'n_pix_grow_sat': 1}, 'ipc': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'superbias': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'refpix': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}, 'rscd': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'type': 'baseline'}, 'firstframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'lastframe': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'linearity': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'dark_current': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'dark_output': None}, 'reset': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}, 'persistence': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'input_trapsfilled': '', 'flag_pers_cutoff': 40.0, 'save_persistence': False, 'save_trapsfilled': True}, 'jump': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}, 'ramp_fit': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}, 'gain_scale': {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}}}
2022-12-04 01:51:01,721 - stpipe.Detector1Pipeline - INFO - Prefetching reference files for dataset: 'ifu_prism_nrs1_uncal.fits' reftypes = ['dark', 'gain', 'linearity', 'mask', 'persat', 'readnoise', 'refpix', 'reset', 'rscd', 'saturation', 'superbias', 'trapdensity', 'trappars']
2022-12-04 01:51:01,730 - stpipe.Detector1Pipeline - INFO - Prefetch for DARK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits'.
2022-12-04 01:51:01,732 - stpipe.Detector1Pipeline - INFO - Prefetch for GAIN reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits'.
2022-12-04 01:51:01,734 - stpipe.Detector1Pipeline - INFO - Prefetch for LINEARITY reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits'.
2022-12-04 01:51:01,736 - stpipe.Detector1Pipeline - INFO - Prefetch for MASK reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits'.
2022-12-04 01:51:01,737 - stpipe.Detector1Pipeline - INFO - Prefetch for PERSAT reference file is 'N/A'.
2022-12-04 01:51:01,738 - stpipe.Detector1Pipeline - INFO - Prefetch for READNOISE reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits'.
2022-12-04 01:51:01,739 - stpipe.Detector1Pipeline - INFO - Prefetch for REFPIX reference file is 'N/A'.
2022-12-04 01:51:01,740 - stpipe.Detector1Pipeline - INFO - Prefetch for RESET reference file is 'N/A'.
2022-12-04 01:51:01,740 - stpipe.Detector1Pipeline - INFO - Prefetch for RSCD reference file is 'N/A'.
2022-12-04 01:51:01,741 - stpipe.Detector1Pipeline - INFO - Prefetch for SATURATION reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits'.
2022-12-04 01:51:01,743 - stpipe.Detector1Pipeline - INFO - Prefetch for SUPERBIAS reference file is '/grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits'.
2022-12-04 01:51:01,745 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPDENSITY reference file is 'N/A'.
2022-12-04 01:51:01,745 - stpipe.Detector1Pipeline - INFO - Prefetch for TRAPPARS reference file is 'N/A'.
2022-12-04 01:51:01,746 - stpipe.Detector1Pipeline - INFO - Starting calwebb_detector1 ...
2022-12-04 01:51:02,279 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:02,281 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx'}
2022-12-04 01:51:02,482 - stpipe.Detector1Pipeline.group_scale - INFO - NFRAMES and FRMDIVSR are equal; correction not needed
2022-12-04 01:51:02,483 - stpipe.Detector1Pipeline.group_scale - INFO - Step will be skipped
2022-12-04 01:51:02,486 - stpipe.Detector1Pipeline.group_scale - INFO - Step group_scale done
2022-12-04 01:51:02,684 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:02,686 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx'}
2022-12-04 01:51:02,715 - stpipe.Detector1Pipeline.dq_init - INFO - Using MASK reference file /grp/crds/cache/references/jwst/jwst_nirspec_mask_0024.fits
2022-12-04 01:51:03,608 - stpipe.Detector1Pipeline.dq_init - INFO - Step dq_init done
2022-12-04 01:51:03,817 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:03,819 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx', 'n_pix_grow_sat': 1}
2022-12-04 01:51:03,844 - stpipe.Detector1Pipeline.saturation - INFO - Using SATURATION reference file /grp/crds/cache/references/jwst/jwst_nirspec_saturation_0020.fits
2022-12-04 01:51:07,064 - stpipe.Detector1Pipeline.saturation - INFO - Detected 37655 saturated pixels
2022-12-04 01:51:07,113 - stpipe.Detector1Pipeline.saturation - INFO - Detected 0 A/D floor pixels
2022-12-04 01:51:07,130 - stpipe.Detector1Pipeline.saturation - INFO - Step saturation done
2022-12-04 01:51:07,324 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:07,327 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': True, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx'}
2022-12-04 01:51:07,327 - stpipe.Detector1Pipeline.ipc - INFO - Step skipped.
2022-12-04 01:51:07,331 - stpipe.Detector1Pipeline.ipc - INFO - Step ipc done
2022-12-04 01:51:07,517 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:07,519 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx'}
2022-12-04 01:51:07,548 - stpipe.Detector1Pipeline.superbias - INFO - Using SUPERBIAS reference file /grp/crds/cache/references/jwst/jwst_nirspec_superbias_0087.fits
2022-12-04 01:51:10,588 - stpipe.Detector1Pipeline.superbias - INFO - Step superbias done
2022-12-04 01:51:10,802 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:10,804 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx', 'odd_even_columns': True, 'use_side_ref_pixels': True, 'side_smoothing_length': 11, 'side_gain': 1.0, 'odd_even_rows': True}
2022-12-04 01:51:10,989 - stpipe.Detector1Pipeline.refpix - INFO - NIR full frame data
2022-12-04 01:51:10,990 - stpipe.Detector1Pipeline.refpix - INFO - The following parameters are valid for this mode:
2022-12-04 01:51:10,990 - stpipe.Detector1Pipeline.refpix - INFO - use_side_ref_pixels = True
2022-12-04 01:51:10,991 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_columns = True
2022-12-04 01:51:10,991 - stpipe.Detector1Pipeline.refpix - INFO - side_smoothing_length = 11
2022-12-04 01:51:10,992 - stpipe.Detector1Pipeline.refpix - INFO - side_gain = 1.0
2022-12-04 01:51:10,992 - stpipe.Detector1Pipeline.refpix - INFO - The following parameter is not applicable and is ignored:
2022-12-04 01:51:10,993 - stpipe.Detector1Pipeline.refpix - INFO - odd_even_rows = False
2022-12-04 01:51:15,129 - stpipe.Detector1Pipeline.refpix - INFO - Step refpix done
2022-12-04 01:51:15,323 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:15,325 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx'}
2022-12-04 01:51:15,350 - stpipe.Detector1Pipeline.linearity - INFO - Using Linearity reference file /grp/crds/cache/references/jwst/jwst_nirspec_linearity_0018.fits
2022-12-04 01:51:19,187 - stpipe.Detector1Pipeline.linearity - INFO - Step linearity done
2022-12-04 01:51:19,370 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:19,372 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx', 'dark_output': None}
2022-12-04 01:51:19,397 - stpipe.Detector1Pipeline.dark_current - INFO - Using DARK reference file /grp/crds/cache/references/jwst/jwst_nirspec_dark_0140.fits
2022-12-04 01:51:24,372 - stpipe.Detector1Pipeline.dark_current - INFO - Science data nints=1, ngroups=10, nframes=1, groupgap=0
2022-12-04 01:51:24,374 - stpipe.Detector1Pipeline.dark_current - INFO - Dark data nints=1, ngroups=10, nframes=1, groupgap=0
2022-12-04 01:51:24,818 - stpipe.Detector1Pipeline.dark_current - INFO - Step dark_current done
2022-12-04 01:51:25,001 - stpipe.Detector1Pipeline.jump - INFO - Step jump running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:25,003 - stpipe.Detector1Pipeline.jump - INFO - Step jump parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx', 'rejection_threshold': 4.0, 'three_group_rejection_threshold': 6.0, 'four_group_rejection_threshold': 5.0, 'maximum_cores': 'none', 'flag_4_neighbors': True, 'max_jump_to_flag_neighbors': 1000.0, 'min_jump_to_flag_neighbors': 10.0, 'after_jump_flag_dn1': 0.0, 'after_jump_flag_time1': 0.0, 'after_jump_flag_dn2': 0.0, 'after_jump_flag_time2': 0.0, 'min_sat_area': 1.0, 'min_jump_area': 5.0, 'expand_factor': 2.0, 'use_ellipses': False, 'sat_required_snowball': True, 'expand_large_events': False}
2022-12-04 01:51:25,014 - stpipe.Detector1Pipeline.jump - INFO - CR rejection threshold = 4 sigma
2022-12-04 01:51:25,030 - stpipe.Detector1Pipeline.jump - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-04 01:51:25,578 - stpipe.Detector1Pipeline.jump - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2022-12-04 01:51:26,923 - stpipe.Detector1Pipeline.jump - INFO - Executing two-point difference method
2022-12-04 01:51:27,013 - stpipe.Detector1Pipeline.jump - INFO - Working on integration 1:
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/twopoint_difference.py:154: RuntimeWarning: All-NaN slice encountered
  max_ratio = np.nanmax(ratio, axis=0)
2022-12-04 01:51:30,666 - stpipe.Detector1Pipeline.jump - INFO - From highest outlier, two-point found 29709 pixels with at least one CR from five or more groups.
2022-12-04 01:51:35,148 - stpipe.Detector1Pipeline.jump - INFO - Total elapsed time = 8.22433 sec
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:302: RuntimeWarning: invalid value encountered in divide
  data /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:303: RuntimeWarning: invalid value encountered in divide
  err /= gain_2d
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/jump/jump.py:304: RuntimeWarning: invalid value encountered in divide
  readnoise_2d /= gain_2d
2022-12-04 01:51:35,273 - stpipe.Detector1Pipeline.jump - INFO - The execution time in seconds: 10.259289
2022-12-04 01:51:35,280 - stpipe.Detector1Pipeline.jump - INFO - Step jump done
2022-12-04 01:51:35,474 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit running with args (<RampModel(1, 10, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:51:35,476 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx', 'int_name': '', 'save_opt': False, 'opt_name': '', 'suppress_one_group': True, 'maximum_cores': 'none'}
2022-12-04 01:51:35,514 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using READNOISE reference file: /grp/crds/cache/references/jwst/jwst_nirspec_readnoise_0019.fits
2022-12-04 01:51:35,515 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using GAIN reference file: /grp/crds/cache/references/jwst/jwst_nirspec_gain_0019.fits
2022-12-04 01:51:35,635 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using algorithm = ols
2022-12-04 01:51:35,635 - stpipe.Detector1Pipeline.ramp_fit - INFO - Using weighting = optimal
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/stcal/ramp_fitting/ols_fit.py:1089: RuntimeWarning: invalid value encountered in multiply
  var_p4[num_int, :, :, :] *= (segs_4[num_int, :, :, :] > 0)
2022-12-04 01:52:22,482 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of groups per integration: 10
2022-12-04 01:52:22,483 - stpipe.Detector1Pipeline.ramp_fit - INFO - Number of integrations: 1
2022-12-04 01:52:22,728 - stpipe.Detector1Pipeline.ramp_fit - INFO - Step ramp_fit done
2022-12-04 01:52:22,880 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:52:22,881 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scale', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx'}
2022-12-04 01:52:22,960 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-04 01:52:22,961 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-04 01:52:22,966 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-04 01:52:23,114 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale running with args (<CubeModel(1, 2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:52:23,116 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': 'gain_scaleints', 'search_output_file': True, 'input_dir': '/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/tmp/tmp366avtnx'}
2022-12-04 01:52:23,189 - stpipe.Detector1Pipeline.gain_scale - INFO - GAINFACT not found in gain reference file
2022-12-04 01:52:23,190 - stpipe.Detector1Pipeline.gain_scale - INFO - Step will be skipped
2022-12-04 01:52:23,195 - stpipe.Detector1Pipeline.gain_scale - INFO - Step gain_scale done
2022-12-04 01:52:23,196 - stpipe.Detector1Pipeline - INFO - ... ending calwebb_detector1
2022-12-04 01:52:23,196 - stpipe.Detector1Pipeline - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 01:52:23,197 - stpipe.Detector1Pipeline - INFO - Step Detector1Pipeline done
2022-12-04 01:52:23,208 - stpipe.AssignWcsStep - INFO - AssignWcsStep instance created.
2022-12-04 01:52:23,329 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:52:23,330 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'sip_approx': True, 'sip_max_pix_error': 0.1, 'sip_degree': None, 'sip_max_inv_pix_error': 0.1, 'sip_inv_degree': None, 'sip_npoints': 12, 'slit_y_low': -0.55, 'slit_y_high': 0.55}
2022-12-04 01:52:23,550 - stpipe.AssignWcsStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2022-12-04 01:52:23,551 - stpipe.AssignWcsStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2022-12-04 01:52:23,552 - stpipe.AssignWcsStep - INFO - theta_y correction: -0.005294283663966503 deg
2022-12-04 01:52:23,553 - stpipe.AssignWcsStep - INFO - theta_x correction: 0.0 deg
2022-12-04 01:52:27,017 - stpipe.AssignWcsStep - INFO - Created a NIRSPEC nrs_ifu pipeline with references {'distortion': None, 'filteroffset': None, 'specwcs': None, 'regions': None, 'wavelengthrange': '/grp/crds/cache/references/jwst/jwst_nirspec_wavelengthrange_0004.asdf', 'camera': '/grp/crds/cache/references/jwst/jwst_nirspec_camera_0004.asdf', 'collimator': '/grp/crds/cache/references/jwst/jwst_nirspec_collimator_0004.asdf', 'disperser': '/grp/crds/cache/references/jwst/jwst_nirspec_disperser_0034.asdf', 'fore': '/grp/crds/cache/references/jwst/jwst_nirspec_fore_0028.asdf', 'fpa': '/grp/crds/cache/references/jwst/jwst_nirspec_fpa_0005.asdf', 'msa': '/grp/crds/cache/references/jwst/jwst_nirspec_msa_0005.asdf', 'ote': '/grp/crds/cache/references/jwst/jwst_nirspec_ote_0005.asdf', 'ifupost': '/grp/crds/cache/references/jwst/jwst_nirspec_ifupost_0004.asdf', 'ifufore': '/grp/crds/cache/references/jwst/jwst_nirspec_ifufore_0003.asdf', 'ifuslicer': '/grp/crds/cache/references/jwst/jwst_nirspec_ifuslicer_0003.asdf'}
2022-12-04 01:52:32,183 - stpipe.AssignWcsStep - INFO - Update S_REGION to POLYGON ICRS  156.176998032 -45.687618307 156.178780407 -45.687618307 156.178780407 -45.686330486 156.176998032 -45.686330486
2022-12-04 01:52:32,186 - stpipe.AssignWcsStep - INFO - COMPLETED assign_wcs
2022-12-04 01:52:32,201 - stpipe.AssignWcsStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 01:52:32,201 - stpipe.AssignWcsStep - INFO - Step AssignWcsStep done
2022-12-04 01:52:32,215 - stpipe.MSAFlagOpenStep - INFO - MSAFlagOpenStep instance created.
2022-12-04 01:52:32,508 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:52:32,510 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-04 01:52:32,532 - stpipe.MSAFlagOpenStep - INFO - Using reference file /grp/crds/cache/references/jwst/jwst_nirspec_msaoper_0001.json
2022-12-04 01:52:32,533 - stpipe.JwstStep - INFO - JwstStep instance created.
2022-12-04 01:52:32,720 - stpipe.MSAFlagOpenStep - INFO - gwa_ytilt is 0.03312480077147484 deg
2022-12-04 01:52:32,721 - stpipe.MSAFlagOpenStep - INFO - gwa_xtilt is 0.3411945700645447 deg
2022-12-04 01:52:32,722 - stpipe.MSAFlagOpenStep - INFO - theta_y correction: -0.005294283663966503 deg
2022-12-04 01:52:32,723 - stpipe.MSAFlagOpenStep - INFO - theta_x correction: 0.0 deg
2022-12-04 01:52:32,739 - stpipe.MSAFlagOpenStep - INFO - SPORDER= 0, wrange=[6e-07, 5.3e-06]
2022-12-04 01:52:32,898 - stpipe.MSAFlagOpenStep - INFO - There are 5 open slits in quadrant 1
2022-12-04 01:52:32,951 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 2
2022-12-04 01:52:32,980 - stpipe.MSAFlagOpenStep - INFO - There are 9 open slits in quadrant 3
2022-12-04 01:52:33,056 - stpipe.MSAFlagOpenStep - INFO - There are 3 open slits in quadrant 4
2022-12-04 01:52:33,084 - stpipe.MSAFlagOpenStep - INFO - There are 0 open slits in quadrant 5
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2585.2572652943927.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2329.91715711254.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2731.341633999907.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2095.6529334650595.
  warnings.warn(f"Invalid interval: upper bound {upper} "
/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/astropy/modeling/bounding_box.py:83: RuntimeWarning: Invalid interval: upper bound 2047.5 is strictly less than lower bound 2085.8983001463794.
  warnings.warn(f"Invalid interval: upper bound {upper} "
2022-12-04 01:52:48,300 - stpipe.MSAFlagOpenStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 01:52:48,301 - stpipe.MSAFlagOpenStep - INFO - Step MSAFlagOpenStep done
2022-12-04 01:52:48,316 - stpipe.SourceTypeStep - INFO - SourceTypeStep instance created.
2022-12-04 01:52:48,816 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:52:48,818 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'source_type': None}
2022-12-04 01:52:48,827 - stpipe.SourceTypeStep - INFO - Input EXP_TYPE is NRS_IFU
2022-12-04 01:52:48,829 - stpipe.SourceTypeStep - INFO - Input SRCTYAPT = UNKNOWN
2022-12-04 01:52:48,829 - stpipe.SourceTypeStep - INFO - Input source type is unknown; setting default SRCTYPE = EXTENDED
2022-12-04 01:52:48,832 - stpipe.SourceTypeStep - INFO - Step SourceTypeStep done
2022-12-04 01:52:48,843 - stpipe.WavecorrStep - INFO - WavecorrStep instance created.
2022-12-04 01:52:49,055 - stpipe.WavecorrStep - INFO - Step WavecorrStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:52:49,057 - stpipe.WavecorrStep - INFO - Step WavecorrStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': ''}
2022-12-04 01:52:49,066 - stpipe.WavecorrStep - INFO - Skipping wavecorr correction for EXP_TYPE NRS_IFU
2022-12-04 01:52:49,069 - stpipe.WavecorrStep - INFO - Step WavecorrStep done
2022-12-04 01:52:49,081 - stpipe.FlatFieldStep - INFO - FlatFieldStep instance created.
2022-12-04 01:52:49,292 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:52:49,294 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'save_interpolated_flat': False, 'user_supplied_flat': None, 'inverse': False}
2022-12-04 01:55:44,456 - stpipe.FlatFieldStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 01:55:44,458 - stpipe.FlatFieldStep - INFO - Step FlatFieldStep done
2022-12-04 01:55:44,469 - stpipe.PathLossStep - INFO - PathLossStep instance created.
2022-12-04 01:55:45,254 - stpipe.PathLossStep - INFO - Step PathLossStep running with args (<IFUImageModel(2048, 2048) from ifu_prism_nrs1_uncal.fits>,).
2022-12-04 01:55:45,256 - stpipe.PathLossStep - INFO - Step PathLossStep parameters are: {'pre_hooks': [], 'post_hooks': [], 'output_file': None, 'output_dir': None, 'output_ext': '.fits', 'output_use_model': False, 'output_use_index': True, 'save_results': False, 'skip': False, 'suffix': None, 'search_output_file': True, 'input_dir': '', 'inverse': False, 'source_type': None}
2022-12-04 01:55:45,284 - stpipe.PathLossStep - INFO - Using PATHLOSS reference file /grp/crds/cache/references/jwst/jwst_nirspec_pathloss_0003.fits
2022-12-04 01:55:45,358 - stpipe.PathLossStep - INFO - Input exposure type is NRS_IFU
2022-12-04 01:56:50,989 - stpipe.PathLossStep - INFO - Results used CRDS context: jwst_1019.pmap
2022-12-04 01:56:50,990 - stpipe.PathLossStep - INFO - Step PathLossStep done

Running test for IFU...
Checking if files exist and obtaining datamodels. This takes a few minutes...
from datamodel  -->     Detector: NRS1   Grating: PRISM   Filter: CLEAR   Lamp: NO_LAMP   EXP_TYPE: NRS_IFU
Using reference file: https://jwst-crds.stsci.edu/unchecked_get/references/jwst/jwst_nirspec_pathloss_0003.fits
got input slices
PLCOR_REF.shape (21, 21, 21)
 Looping through the slices... 
working with slice 0
SHAPES (40, 439) (39, 438)
ALTERED SHAPE OF SLICE: V2
ALTERED SHAPE OF SLICE: V6
final left 780, right 819, top 999, bottom 561
NEW SHAPE OF SLICE: (39, 438) and corr_vals.shape: (39, 438)

/internal/data1/jenkins/workspace/Notebooks/jwst_validation_notebooks_spacetelescope/miniconda3/envs/jwst_validation_notebooks/lib/python3.9/site-packages/nirspec_pipe_testing_tool/calwebb_spec2_pytests/auxiliary_code/pathloss_ifu_uni.py:168: RuntimeWarning: invalid value encountered in divide
  pathloss_divided = comp_sci/previous_sci

working with slice 1
SHAPES (41, 441) (40, 442)
ALTERED SHAPE OF SLICE: V2
ALTERED SHAPE OF SLICE: V8
final left 1197, right 1237, top 946, bottom 504
NEW SHAPE OF SLICE: (40, 442) and corr_vals.shape: (40, 442)

working with slice 2
SHAPES (40, 438) (39, 438)
ALTERED SHAPE OF SLICE: V2
final left 730, right 769, top 1005, bottom 567
NEW SHAPE OF SLICE: (39, 438) and corr_vals.shape: (39, 438)

working with slice 3
SHAPES (41, 442) (40, 442)
ALTERED SHAPE OF SLICE: V2
final left 1246, right 1286, top 940, bottom 498
NEW SHAPE OF SLICE: (40, 442) and corr_vals.shape: (40, 442)

working with slice 4
SHAPES (40, 437) (39, 438)
ALTERED SHAPE OF SLICE: V2
ALTERED SHAPE OF SLICE: V8
final left 681, right 720, top 1010, bottom 572
NEW SHAPE OF SLICE: (39, 438) and corr_vals.shape: (39, 438)

working with slice 5
SHAPES (41, 442) (40, 442)
ALTERED SHAPE OF SLICE: V2
final left 1295, right 1335, top 933, bottom 491
NEW SHAPE OF SLICE: (40, 442) and corr_vals.shape: (40, 442)

working with slice 6
SHAPES (40, 437) (39, 438)
ALTERED SHAPE OF SLICE: V2
ALTERED SHAPE OF SLICE: V8
final left 632, right 671, top 1016, bottom 578
NEW SHAPE OF SLICE: (39, 438) and corr_vals.shape: (39, 438)


# Quickly see if the test passed 

print('These are the final results of the tests: ')
for key, val in results_dict.items():
    if not isinstance(val, str):
        if val:
            val = 'PASSED'
        else:
            val = 'FAILED'
    print('{:<42} {:<8}'.format(key, val))

These are the final results of the tests: 
ifu_prism_nrs1_uncal.fits                  All slits PASSED path_loss test.
ifu_prism_nrs2_uncal.fits                  skipped

JWST Pipeline Validation Testing Notebook: spec2, pathloss step for ifu prism¶

Table of Contents¶

Imports¶

Test Description¶

Results¶

Calibration WG Requested Algorithm:¶

Defining Term¶

Run the JWST pipeline and pathloss validation tests¶

Testing Data Set¶

About this Notebook¶